Research workbench
X-ray crystal structure of RV2018 from mycobacterium tuberculosis
Analyse X-ray crystal structure of RV2018 from mycobacterium tuberculosis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AF3
- Type
- protein
- Length
- 428 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VAPBC49
- UniProt
- O53464
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VAPBC49 | protein | 214 | 51% helix, 14% strand | O53464 |
| B | VAPBC49 | protein | 214 | 52% helix, 14% strand | O53464 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 645 | 0.67 | 0.76 | 55 | empty |
| 2 | 79 | 0.42 | 0.80 | 21 | empty |
| 3 | 60 | 0.35 | 0.78 | 15 | empty |
| 4 | 57 | 0.35 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1003 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5AF3 · X-ray crystal structure of RV2018 from mycobacterium tuberculosis · the same entry in another collection · chain A against A, TM-score 1.00
- O53464 · AlphaFold monomer V2.0 prediction for putative antitoxin VAPB45 (O53464) · a predicted model of the same protein · chain B against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O53464
- Elsewhere: RCSB PDB 5AF3 · PDBe 5AF3 · UniProt O53464
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.